Dynamic report for checking simulation design (4.5)

True mean Progression Free Time (PFT)

     Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
----         7.11        7.11        7.11        7.11      7.11
---+         7.11        7.11        7.11        7.11      7.11
--+-         7.11        7.11        7.11        7.11      7.11
--++         7.11        7.11        7.11        7.11      7.11
-+--         7.11        7.11        7.11        7.11      7.11
-+-+         7.11        7.11        7.11        7.11      7.11
-++-         7.11        7.11        7.11        7.11      7.11
-+++         7.11        7.11        7.11        7.11      7.11
+---         7.11        7.11        7.11        7.11      7.11
+--+         7.11        7.11        7.11        7.11      7.11
+-+-         7.11        7.11        7.11        7.11      7.11
+-++         7.11        7.11        7.11        7.11      7.11
++--         7.11        7.11        7.11        7.11      7.11
++-+         7.11        7.11        7.11        7.11      7.11
+++-         7.11        7.11        7.11        7.11      7.11


Graduation output

$superiority
            Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all                    0           0           0           0         0
TP53- & AR-            0           0           0           0         0
TP53+                  0           0           0           0         0
DRD+                   0           0           0           0         0
TEfus+                 0           0           0           0         0

$inferiority
            Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all                    0           0           0           0         0
TP53- & AR-            0           0           0           0         0
TP53+                  0           0           0           0         0
DRD+                   0           0           0           0         0
TEfus+                 0           0           0           0         0


Final probability of superioriry by signatures and biomarkers subtypes

$p_sign
            Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all                 0.46        0.28        0.39        0.34      0.32
TP53- & AR-         0.68        0.35        0.20        0.55      0.60
TP53+               0.42        0.41        0.41        0.41      0.37
DRD+                0.12        0.14        0.17        0.14      0.20
TEfus+              0.36        0.25        0.39        0.28      0.21

$p_type
     Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
----         1.00        0.89        0.49        0.98      0.94
---+         0.80        0.61        0.70        0.82      0.34
--+-         0.50        0.77        0.67        0.39      0.49
--++         0.87        0.52        0.52        0.72      0.64
-+--         0.16        0.14        0.09        0.23      0.46
-+-+         0.43        0.42        0.34        0.29      0.55
-++-         0.54        0.48        0.63        0.61      0.48
-+++         0.11        0.15        0.13        0.19      0.13
+---         0.91        0.53        0.67        0.80      0.74
+--+         0.26        0.32        0.64        0.23      0.22
+-+-         0.51        0.49        0.51        0.52      0.58
+-++         0.55        0.57        0.61        0.58      0.60
++--         0.16        0.29        0.45        0.21      0.16
++-+         0.41        0.48        0.54        0.36      0.45
+++-         0.54        0.55        0.48        0.44      0.52








     Control Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
----      98           86          71          31          74        61
---+      15            6           7          12          16        10
--+-      39           37          27          30          24        27
--++      14           22          18           8          21        20
-+--      18            5           5          10           6        16
-+-+       8            8          12           8           6        13
-++-       0            3           1           4           1         1
-+++       3            1           0           3           2         1
+---      10           11           6           5           9         8
+--+       4            5           6           8           8         7
+-+-       0            1           0           0           1         3
+-++       8            6           3           3           5         4
++--      11            3           3           4           2         3
++-+       2            2           4           3           1         0
+++-       4            0           3           4           1         0
            Control Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all             234          196         166         133         177       174
TP53- & AR-     139          105          95          61         102       100
TP53+            68           70          52          52          55        56
DRD+             46           22          28          36          19        34
TEfus+           54           50          50          45          59        55





Number of events, PT, and rate by subtype (over time)




Number of events, PT, and rate by signature (over time)



Analysis of final simulated results

Sample of 10 rows:

      id          trt         trt2 line subtype delta month0     time_m all TP53- & AR- TP53+ DRD+ TEfus+
790  720    Docetaxel    Docetaxel    1    +-++     1     23  7.5639230   1           0     1    0      1
272  252  Abiraterone  Abiraterone    1    ----     1      8  4.5849921   1           1     0    0      0
13    13 Enzalutamide Enzalutamide    1    --++     1      0 16.2484093   1           0     1    0      1
804  731 Enzalutamide Enzalutamide    1    --++     0     24 12.0000000   1           0     1    0      1
719  654  Cabazitaxel  Cabazitaxel    1    ----     1     21  4.6382168   1           1     0    0      0
930  845      Control Enzalutamide    1    ++--     1     28  2.9078370   1           0     0    1      0
931  846      Control    Docetaxel    1    ++--     1     28  0.9312359   1           0     0    1      0
186  172  Cabazitaxel  Cabazitaxel    1    --+-     1      5 10.1360198   1           0     1    0      0
55    55  Cabazitaxel  Cabazitaxel    1    --+-     1      1  8.4867349   1           0     1    0      0
1010 919  Cabazitaxel  Cabazitaxel    1    ----     0     30  6.0000000   1           1     0    0      0

Descriptives

Mean number of progressions and follow-up time:

$all
# A tibble: 6 x 4
  trt          progressions    PT  rate
  <fct>               <dbl> <dbl> <dbl>
1 Control               216 1524. 0.142
2 Enzalutamide          180 1555. 0.116
3 Abiraterone           142 1032. 0.138
4 Carboplatin           117  842. 0.139
5 Cabazitaxel           163 1242. 0.131
6 Docetaxel             151 1120. 0.135

$`TP53- & AR-`
# A tibble: 6 x 4
  trt          progressions    PT  rate
  <fct>               <dbl> <dbl> <dbl>
1 Control               129  874. 0.148
2 Enzalutamide           91  863. 0.105
3 Abiraterone            83  609. 0.136
4 Carboplatin            58  351. 0.165
5 Cabazitaxel            92  759. 0.121
6 Docetaxel              82  668. 0.123

$`TP53+`
# A tibble: 6 x 4
  trt          progressions    PT  rate
  <fct>               <dbl> <dbl> <dbl>
1 Control                62  471. 0.132
2 Enzalutamide           67  543. 0.123
3 Abiraterone            41  328. 0.125
4 Carboplatin            41  329. 0.125
5 Cabazitaxel            50  374. 0.134
6 Docetaxel              52  378. 0.137

$`DRD+`
# A tibble: 6 x 4
  trt          progressions    PT   rate
  <fct>               <dbl> <dbl>  <dbl>
1 Control                34  381. 0.0892
2 Enzalutamide           23  147. 0.157 
3 Abiraterone            27  193. 0.140 
4 Carboplatin            32  235. 0.136 
5 Cabazitaxel            17  109. 0.156 
6 Docetaxel              28  245. 0.114 

$`TEfus+`
# A tibble: 6 x 4
  trt          progressions    PT  rate
  <fct>               <dbl> <dbl> <dbl>
1 Control                49  361. 0.136
2 Enzalutamide           50  399. 0.125
3 Abiraterone            47  310. 0.152
4 Carboplatin            39  294. 0.133
5 Cabazitaxel            54  381. 0.142
6 Docetaxel              54  342. 0.158

Kaplan-Meier results:

$all
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)

                   n events median 0.95LCL 0.95UCL
trt=Control      259    216   5.10    4.11    6.29
trt=Enzalutamide 216    180   6.05    5.01    7.34
trt=Abiraterone  178    142   5.21    4.41    6.63
trt=Carboplatin  147    117   5.81    4.29    7.23
trt=Cabazitaxel  198    163   5.23    4.44    6.24
trt=Docetaxel    190    151   5.74    4.92    6.97

$`TP53- & AR-`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)

                   n events median 0.95LCL 0.95UCL
trt=Control      152    129   5.06    3.57    6.39
trt=Enzalutamide 115     91   6.62    5.89    8.38
trt=Abiraterone  101     83   5.39    4.49    7.66
trt=Carboplatin   69     58   3.46    2.34    6.78
trt=Cabazitaxel  115     92   5.60    4.41    7.78
trt=Docetaxel    108     82   6.44    4.92    8.48

$`TP53+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)

                  n events median 0.95LCL 0.95UCL
trt=Control      75     62   5.71    3.63    7.09
trt=Enzalutamide 76     67   4.83    4.06    7.60
trt=Abiraterone  56     41   5.83    3.77    8.26
trt=Carboplatin  56     41   6.86    4.57    9.08
trt=Cabazitaxel  60     50   5.23    4.44    9.16
trt=Docetaxel    63     52   5.74    4.45    7.69

$`DRD+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)

                  n events median 0.95LCL 0.95UCL
trt=Control      50     34   7.86    6.29   11.24
trt=Enzalutamide 25     23   5.94    4.28    8.35
trt=Abiraterone  31     27   4.41    2.88    9.19
trt=Carboplatin  43     32   5.79    3.39    8.68
trt=Cabazitaxel  20     17   2.28    1.56      NA
trt=Docetaxel    36     28   5.24    2.96   12.78

$`TEfus+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)

                  n events median 0.95LCL 0.95UCL
trt=Control      59     49   5.73    3.46    7.65
trt=Enzalutamide 59     50   5.59    4.04    8.39
trt=Abiraterone  56     47   5.39    3.55    7.15
trt=Carboplatin  50     39   5.93    2.37    9.08
trt=Cabazitaxel  65     54   4.44    3.76    7.37
trt=Docetaxel    62     54   4.86    2.68    6.95